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In all experimental sciences, the precision and reliability of quantitative measurements are paramount. This is particularly true when examining the interactions between small molecules and biomolecules/polyelectrolytes, such as DNAs/RNAs, and yet it is overlooked in most publications of thermodynamic binding parameters. This paper presents findings from COST Action 18202 "Network for Equilibria and Chemical Thermodynamics Advanced Research," which assessed the consistency of data derived from the interactions of calf-thymus DNA (CT-DNA) with the fluorescent intercalator ethidium bromide (EB) through spectrofluorimetric titrations. We first discuss critical experimental aspects and propose a reference experimental protocol which can be used to calibrate procedures for the determination of nucleic acid binding equilibrium constants. We then fit the experimental points according to different procedures and analyse the results focusing on the statistical dispersion of the data, aiming at enlightening the strong and weak points of different fitting procedures. The implications of this work are significant, demonstrating how the statistical dispersion of experimental data can influence the interpretation of biochemical coordination mechanisms. Our study reveals that, despite rigorous protocol standardization, the determination of binding parameters remains sensitive to the choice of data fitting method, with deviations in the logarithmic stability constant (logK) values not falling below 5 % relative standard deviation (RSD), or ± 0.5 logK units for 95 % confidence. This variability evidences the critical need for standardized best practices in data treatment as well as experimental procedures. Although our study focuses on the EB/CT-DNA system through fluorescence titrations, the broader implications for other methodologies across various biochemical systems highlight the importance of this first-of-its-kind inter-laboratory comparison in advancing our understanding of biochemical coordination processes., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: All authors reports administrative support was provided by European Cooperation in Science and Technology. Eva A. Enyedy, Orsolya Domotor reports financial support was provided by National Research, Development and Innovation Office-NKFIA. E. Garcia Espana, J. Garcia reports financial support was provided by Consellería de Universidades, Ciencia y Sociedad Digital of the Generalitat Valenciana. I. Correia, N. Ribeiro, N. Basilio reports financial support was provided by Foundation for Science and Technology - Portugal. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Citrate (Cit) and Deferoxamine B (DFOB) are two important organic ligands coexisting in soils with distinct different affinities for metal ions. It has been theorized that siderophores and weak organic ligands play a synergistic role during the transport of micronutrients in the rhizosphere, but the geochemical controls of this process remain unknown. Here we test the hypothesis that gradients in pH and ion strength regulate and enable the cooperation. To this end, first we use potentiometric titrations to identify the dominant Zn(II)-Cit and Zn(II)-DFOB complexes and to determine their ionic strength dependent stability constants between 0 and 1 mol dm -3 . We parametrise the Extended Debye-Hückel (EDH) equation and determine accurate intrinsic association constants (logβ 0 ) for the formation of the complexes present. The speciation model developed confirms the presence of [Zn(Cit)] - , [Zn(HCit)], [Zn 2 (Cit) 2 (OH) 2 ] 4- , and [Zn(Cit) 2 ] 4- , with [Zn(Cit)] - and [Zn 2 (Cit) 2 (OH) 2 ] 4- the dominant species in the pH range relevant to rhizosphere. We propose the existence of a new [Zn(Cit)(OH) 3 ] 4- complex above pH 10. We also verify the existence of two hexadentate Zn(II)-DFOB species, i.e., [Zn(DFOB)] - and [Zn(HDFOB)], and of one tetradentate species [Zn(H 2 DFOB)] + . Second, we identify the pH and ionic strength dependent ligand exchange points (LEP) of Zn with citrate and DFOB and the stability windows for Zn(II)-Cit and Zn(II)-DFOB complexes in NaCl and rice soil solutions. We find that the LEPs fall within the pH and ionic strength gradients expected in rhizospheres and that the stability windows for Zn(II)-citrate and Zn(II)-DFOB, i.e., low and high affinity ligands, can be distinctly set off. This suggests that pH and ion strength gradients allow for Zn(II) complexes with citrate and DFOB to dominate in different parts of the rhizosphere and this explains why mixtures of low and high affinity ligands increase leaching of micronutrients in soils. Speciation models of soil solutions using newly determined association constants demonstrate that the presence of dissolved organic matter and inorganic ligands (i.e., bicarbonate, phosphate, sulphate, or chlorides) do neither affect the position of the LEP nor the width of the stability windows significantly. In conclusion, we demonstrate that cooperative and synergistic ligand interaction between low and high affinity ligands is a valid mechanism for controlling zinc transport in the rhizosphere and possibly in other environmental reservoirs such as in the phycosphere. Multiple production of weak and strong ligands is therefore a valid strategy of plants and other soil organisms to improve access to micronutrients., (© 2022. The Author(s).)

In Myotonic Dystrophy type 1 (DM1), a non-coding CTG repeats rare expansion disease; toxic double-stranded RNA hairpins sequester the RNA-binding proteins Muscleblind-like 1 and 2 (MBNL1 and 2) and trigger other DM1-related pathogenesis pathway defects. In this paper, we characterize four D-amino acid hexapeptides identified together with abp1, a peptide previously shown to stabilize CUG RNA in its single-stranded conformation. With the generalized sequence cpy(a/t)(q/w)e, these related peptides improved three MBNL-regulated exon inclusions in DM1-derived cells. Subsequent experiments showed that these compounds generally increased the relative expression of MBNL1 and its nuclear-cytoplasmic distribution, reduced hyperactivated autophagy, and increased the percentage of differentiated (Desmin-positive) cells in vitro. All peptides rescued atrophy of indirect flight muscles in a Drosophila model of the disease, and partially rescued muscle function according to climbing and flight tests. Investigation of their mechanism of action supports that all four compounds can bind to CUG repeats with slightly different association constant, but binding did not strongly influence the secondary structure of the toxic RNA in contrast to abp1. Finally, molecular modeling suggests a detailed view of the interactions of peptide-CUG RNA complexes useful in the chemical optimization of compounds., (© 2021. The Author(s).)

Bacteria, fungi and grasses use siderophores to access micronutrients. Hence, the metal binding efficiency of siderophores is directly related to ecosystem productivity. Salinization of natural solutions, linked to climate change induced sea level rise and changing precipitation patterns, is a serious ecological threat. In this study, we investigate the impact of salinization on the zinc(II) binding efficiency of the major siderophore functional groups, namely the catecholate (for bacterial siderophores), α-hydroxycarboxylate (for plant siderophores; phytosiderophores) and hydroxamate (for fungal siderophores) bidentate motifs. Our analysis suggests that the order of increasing susceptibility of siderophore classes to salinity in terms of their zinc(II) chelating ability is: hydroxamate < catecholate < α-hydroxycarboxylate. Based on this ordering, we predict that plant productivity is more sensitive to salinization than either bacterial or fungal productivity. Finally, we show that previously observed increases in phytosiderophore release by barley plants grown under salt stress in a medium without initial micronutrient deficiencies, are in line with the reduced zinc(II) binding efficiency of the α-hydroxycarboxylate ligand and hence important for the salinity tolerance of whole-plant zinc(II) status., (© 2021. The Author(s).)

Anion-π interactions are emerging as exotic features with potential applications in chemistry. In the last years, their relevance in living systems has been outlined, and so far there is no concluding significant evidence recognized about the participation of anion-π interactions in water because anion-π sensors contain large aromatic hydrophobic surfaces with limited solubility. By transforming a neutral heterocycle (for example quinoline) into its corresponding salt (quinolinium), we have been able to overcome these solubility issues, and new cationic water-soluble fluorophores have been prepared. Herein, we used N-alkylated heterocycles as π-acidic surfaces to shed light on the nature of anion-π in water by the direct measurement of the fluorescence and UV/Vis spectra in combination with DFT and X-ray analyses.

Micronutrient deficiencies threaten global food production. Attempts to biofortify crops rely on a clear understanding of micronutrient uptake processes. Zinc deficiency in rice is a serious problem. One of the pathways proposed for the transfer of zinc from soils into rice plants involves deoxymugineic acid (DMA), a phytosiderophore. The idea that phytosiderophores play a wider role in nutrition of Poaceae beyond iron is well established. However, key mechanistic details of the DMA-assisted zinc uptake pathway in rice remain uncertain. In particular, questions surround the form in which zinc from DMA is taken up [i.e. as free aqueous Zn(II) or as Zn(II)-DMA complexes] and the role of competitive behaviour of other metals with DMA. We propose that an accurate description of the effect of changes in pH, ligand concentration, and ionic strength on the stability of Zn(II)-DMA complexes in the presence of other metals in the microenvironment around root cells is critical for understanding the modus operandi of DMA during zinc uptake. To that end, we reveal the importance of geochemical changes in the microenvironment around root cells and demonstrate the effect of inaccurate stability constants on speciation models., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Atherosclerosis is the major underlying pathologic cause of coronary artery disease. An early detection of the disease can prevent clinical sequellae such as angina, myocardial infarction, and stroke. The different imaging techniques employed to visualize the atherosclerotic plaque provide information of diagnostic and prognostic value. Furthermore, the use of contrast agents helps to improve signal-to-noise ratio providing better images. For nuclear imaging techniques and optical imaging these agents are absolutely necessary. We report on the different contrast agents that have been used, are used or may be used in future in animals, humans, or excised tissues for the distinct imaging modalities for atherosclerotic plaque imaging.

The dinucleating ligand L (1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-ol) combined with metal ions efficiently cleaves DNA when M : L is 1 : 1 (M = Co(II) or Fe(III)) at pH 5.5-7.0, with free L being more active at acidic pH than when bound to Zn(II), Cu(II) or Ni(II) at neutral pH.

The synthesis of new 1,4-bisalkylamino (2-4) and 1-alkylamino-4-chloro (5-6) substituted benzo[g]phthalazines is reported. Compounds 2-4 and 6 were prepared both in the free and heteroaromatic ring protonated forms. Bifunctional 6 contains the 1,4-bisaminopropylpiperazine chain as a linker between the two heteroaromatic units, whereas 5 is its monofunctional analogue. The in vitro antitumour activity of the synthesized compounds has been tested against human colon, breast and lung carcinoma cells, and also against human glioblastoma cells. Results obtained show that all of them are active in all cases, but bifunctional 6.2HCl is remarkably effective against the four cell lines tested, exhibiting IC50 values in the range of 10(-7) M, similar to those found for doxorubicin. The bifunctional structure of 6.2HCl enhances activity with respect to the monofunctional related compounds 5 and 7, leading to the highest activity among all the compounds tested. Molecular modelling of 6 suggests that those results could be indicative of DNA bisintercalation, which should be specially favoured in the diprotonated form 6.2HCl, a compound suitable for being studied more in depth in further biological tests. Measure of the DNA thermal melting curves show that the linear rise in Tm for bifunctional 6.2HCl is nearly twice than that one obtained for monofunctional 5, and supports the DNA-binding hypothesis., (Copyright (c) 2010 Elsevier Ltd. All rights reserved.)

The interaction of the biologically relevant anions deriving from the six pyridinedicarboxylic acids (H2PDC) with two macrocyclic receptors containing a pentamine chain and a bipyridine (1) or a phenanthroline (2) moiety, as well as with the aliphatic analogue [21]aneN7 (3), was studied by means of spectroscopic methods (UV-vis, NMR) and potentiometric titrations affording the stability constants of the adducts formed. All three receptors form stable complexes with the substrates thanks to the formation of several salt bridges and hydrogen bond contacts, as observed in the crystal structure of the H8[3(2,6-PDC)4] x H2O x 0.5 EtOH solid compound. Additional pi-stacking interactions between the aromatic moieties of substrates and receptors enhance the stability of complexes with 1 and 2. Compounds 1 and 2 show a marked selectivity toward 2,6-pyridinedicarboxylate anions. In particular, 1 is able to perform a very efficient recognition of these species in the presence of 2 and 3. Molecular modeling calculations suggested that such recognition ability of 1 can be ascribed to a superior structural and electrostatic complementarity with the substrate compared to 2 and 3.

The Zn(2+) coordination chemistry and luminescent behavior of two ligands constituted by an open 1,4,7-triazaheptane chain functionalized at both ends with 2-picolyl units and either a methylnaphthyl (L1) or a dansyl (L2) fluorescent unit attached to the central amino nitrogen are reported. The fluorescent properties of the ZnL1(2+) and ZnL2(2+) complexes are then exploited toward detection of anions. L1 in the pH range of study has four protonation constants. The fluorescence emission from the naphthalene fluorophore is quenched either at low or at high pH values leading to an emissive pH window centered around pH = 5. In contrast, in L2 the fluorescence emission from the dansyl unit occurs only at basic pH values. In the case of L1, a red-shifted band appearing in the visible region was assigned to an exciplex emission involving the naphthalene and the tertiary amine of the polyamine chain. L1 forms Zn(2+) mononuclear complexes of ZnH(p)L1((p+2)+) stoichiometry with p = 1, 0, -1. Formation of the ZnL1(2+)species produces a strong enhancement of the L1 luminescence leading to an extended emissive pH window from pH = 5 to pH = 9. Addition of several anions to this last complex leads to a partial quenching effect. On the contrary, the fluorescence emission of L2 is partially quenched upon complexation with Zn(2+) in the same pH window (5 < pH < 9). The lower stability of ZnL2(2+) with respect to ZnL1(2+) suggests a lack of involvement of the sulfonamide group in the first coordination sphere. However, there is spectral evidence for an interesting photoinduced binding of the sulfonamide nitrogen to Zn(2+). While addition of diphosphate, triphosphate, citrate, and D,L-isocitrate to a solution of ZnL2(2+) restores the fluorescence emission of the system (lambda max ca. 600 nm), addition of phosphate, chloride, iodide, and cyanurate do not produce any significant change in fluorescence. Moreover, this system would permit one to differentiate diphosphate and triphosphate over citrate and d, l-isocitrate because the fluorescence enhancement observed upon addition of the first anions is much sharper. The ZnL2(2+) complex and its mixed complexes with diphosphate, triphosphate, citrate, and D,L-isocitrate have been characterized by (1)H, (31)P NMR, and Electrospray Mass Spectrometry.